MICROPHERRET: MICRObial PHEnotypic tRait ClassifieR using Machine lEarning Techniques DOI Creative Commons
Edoardo Bizzotto,

Sofia Fraulini,

Guido Zampieri

et al.

Environmental Microbiome, Journal Year: 2024, Volume and Issue: 19(1)

Published: Aug. 8, 2024

In recent years, there has been a rapid increase in the number of microbial genomes reconstructed through shotgun sequencing, and obtained by newly developed approaches including metagenomic binning single-cell sequencing. However, our ability to functionally characterize these experimental assays is orders magnitude less efficient. Consequently, pressing need for development swift automated strategies functional classification genomes.

Language: Английский

Cross-sectional-dependent microbial assembly and network stability: Bacteria sensitivity response was higher than eukaryotes and fungi in the Danjiangkou Reservoir DOI
Wan-Ping Wang, Rongxin Wang,

Yuying Li

et al.

Journal of Environmental Management, Journal Year: 2025, Volume and Issue: 379, P. 124851 - 124851

Published: March 7, 2025

Language: Английский

Citations

0
Effects of water-saving irrigation on microbial community structures, assembly, and metabolic activities in alfalfa rhizosphere soils DOI
Feng Ding,

Shun Ji,

Renna Sa

et al.

International Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: May 9, 2025

Language: Английский

Citations

0
Carbon Nanodot–Microbe–Plant Nexus in Agroecosystem and Antimicrobial Applications DOI Creative Commons
József Prokisch, Duyen H. H. Nguyen, Arjun Muthu

et al.

Nanomaterials, Journal Year: 2024, Volume and Issue: 14(15), P. 1249 - 1249

Published: July 25, 2024

The intensive applications of nanomaterials in the agroecosystem led to creation several environmental problems. More efforts are needed discover new insights nanomaterial-microbe-plant nexus. This relationship has dimensions, which may include transport different plant organs, nanotoxicity soil microbes and plants, possible regulations. review focuses on challenges prospects nexus under conditions. previous nano-forms were selected this study because rare, published articles such nanomaterials. Under study's nexus, more carbon nanodot-microbe-plant discussed along with role frontier nano-tellurium-microbe Transport organs applications, translocation these nanoparticles besides their expected will be also reported current study. Nanotoxicity plants was investigated by taking account morpho-physiological, molecular, biochemical concerns. highlights regulations a focus risk at ecological level risks human health, scientific organizational levels. opens many windows studies near future.

Language: Английский

Citations

2
Characterization of bacterial community dynamics dominated by salinity in lakes of the Inner Mongolian Plateau, China DOI Creative Commons
Xin Guo,

Xiaohong Shi,

Shi Yujiao

et al.

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: Aug. 21, 2024

Microorganisms in lakes are sensitive to salinity fluctuations. Despite extensive prior research on bacterial communities, our understanding of their characteristics and assembly mechanisms lakes, especially desert with different salinities. To address this issue, we collected three samples from freshwater six brackish five salt the Badanjilin Desert. The 16S rRNA gene sequencing was applied investigate interactions rising salinity, community coexistence patterns, mechanisms. Our findings suggested that increased lake significantly reduces diversity enhanced differentiation. Significant variations were observed contribution biomarkers Cyanobacteria, Chloroflexi, Halobacterota composition communities. communities exhibited a higher susceptibility limitations than those lakes. In addition, null modeling analyses confirmed quantitative biases stochastic processes across freshwater, brackish, saline With increasing significance undominated diffusion limitation decreased slightly, influence homogenizing dispersal increased. However, stochasticity remained dominant process all analysis co-occurring networks revealed reduced complexity network structures altered interspecific interactions, resulting interspecies collaboration levels. Under stress, key taxon Cyanobacteria ( Schizothrix_LEGE_07164 ) replaced by Proteobacteria Thalassobaculum Polycyclovorans Thermotogota SC103 results indicated symbiotic patterns varying gradients offer insights into potential aggregation, thereby enhancing distribution response changes.

Language: Английский

Citations

1
Unraveling the relationship between plant species and physicochemical properties on rhizosphere and rhizoplane fungal communities in alpine wet meadows DOI Creative Commons
Awais Iqbal, Muhammad Maqsood Ur Rehman, Muhammad Usman

et al.

Environmental Sciences Europe, Journal Year: 2023, Volume and Issue: 35(1)

Published: Dec. 21, 2023

Abstract Background Wet meadows, a type of wetland, are impacted by significant climate fluctuation and human activity, impacting soil microorganisms that play an essential role in ecosystem processes. Understanding the underlying ecological mechanisms processes wet meadows depends on fungal communities associated with plant roots. We used Illumina MiSeq profiling for amplicon sequencing to determine how environmental factors elevation affect rhizosphere rhizoplane related three species, Cremanthodium ellisii, lineare , Caltha s caposa, alpine meadows. Results The phyla Ascomycota Basidiomycota dominated (54.5% 20.9%) (51.6% 36.4%), while predominant genera were Unclassified fungi Ascomycota, Pseudeurotium Tetracladium, Vishniacozyma, Rhodotorula, Cadophora, Penicillium . Mantel test network analysis revealed water content (SWC), organic carbon (SOC), total nitrogen (TN) primary drivers communities. However, influence microbial biomass C (MBC), pH, N (MBN), varied. Stochastic assembly dominant both FUNGuild functional prediction site-specific variation trophic level guild plant-root-associated contained 58.5% saprotrophs, 11.7% pathotrophs, 12.6% symbiotrophs. In addition, 60.4% observed OTUs arbuscular mycorrhizae, 13.2% endophytes, 20.9% ectomycorrhizae, 1.09% orchid mycorrhizae. comprised 51.3% linked 13.9% 7.92% Moreover, 36.1% represented 25.0% 30.6% 2.77% ascribed mycorrhizae rhizoplane. abundance saprotrophs pathotrophs was highest C. ellisii at SI SIII, symbiotrophs SIII. Similar variations among species sites groups (guilds). Conclusions It concluded although root compartments significantly influenced rhizoplane, types exhibited distinct effects. This study explains physicochemical properties, can alter overall structure repertoire Graphical

Language: Английский

Citations

2
Immobilization of phosphorus in sediment-water system by hydrous iron oxide and hydrous iron oxide/calcite mixture under feed input condition DOI

Lingui Li,

Yanhui Zhan,

Jianwei Lin

et al.

Journal of Environmental Sciences, Journal Year: 2024, Volume and Issue: unknown

Published: June 1, 2024

Language: Английский

Citations

0
MICROPHERRET: MICRObial PHEnotypic tRait ClassifieR using Machine lEarning Techniques DOI Creative Commons
Edoardo Bizzotto,

Sofia Fraulini,

Guido Zampieri

et al.

Environmental Microbiome, Journal Year: 2024, Volume and Issue: 19(1)

Published: Aug. 8, 2024

In recent years, there has been a rapid increase in the number of microbial genomes reconstructed through shotgun sequencing, and obtained by newly developed approaches including metagenomic binning single-cell sequencing. However, our ability to functionally characterize these experimental assays is orders magnitude less efficient. Consequently, pressing need for development swift automated strategies functional classification genomes.

Language: Английский

Citations

0